Michael Nagy

No apologies needed! I totally understand, and you've honestly been extremely generous with your support over the course of my use of your program!

Hi All! I know that this codebase is no longer maintained but figured I'd still share this in case somewhat can help or has any thoughts. Essentially on one of my bam files, which for all purposes doesn't appear to be any different than the hundreds of others I've run, encountered an error I've never seen before. Wed Aug 2 16:59:16 2023: Generate non-split read BED Wed Aug 2 16:59:23 2023: Process hash to get best deletion/duplication candidates Wed Aug 2 16:59:28 2023: Build split read clusters...

Is it an issue that my bams are in HG38? it seems like most of the reference files for mitosalt are hg19....

UPDATE: I changed the config file to look for chrM, not MT, as that is how MT reads are described in my HG38 FASTA. That seems to have done the trick. Thanks!

hello! Thanks for suggestions, I started a run using the modifications and below was the log output orihe = 407 [23/187] orils = 5730 orile = 5763 score_threshold = 80 evalue_threshold = 0.00001 split_length = 15 paired_distance = 1000 deletion_threshold_min = 30 deletion_threshold_max = 30000 breakthreshold = -2 cluster_threshold = 5 breakspan = 15 sizelimit = 10000 hplimit = 0.01 flank = 15 split_distance_threshold = 5 dna = yes enriched = no nu_mt = yes rmtmp = yes o_mt = yes i_del = yes cn_mt...

Hi All, I implemented the suggested changes, and encountered the following issues. Wed Nov 30 17:11:40 2022: Map to NU+MT genome Wed Nov 30 17:11:40 2022: Extract reads [E::hts_open_format] Failed to open file tmp_A0719.sam samtools view: failed to open "tmp_A0719.sam" for reading: No such file or directory [main_samview] region "MT" specifies an unknown reference name. Continue anyway. Wed Nov 30 17:11:40 2022: Create FASTQ [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed...

Hello, In our pipeline we generate Bam files through Illumina's Dragen aligner. Would it be possible to modify Mitosalt to intake these files? Henceforth, skipping the alignment steps involved with fastqs. I'm happy to modify the logic of the program myself, if given some direction on how to tackle the problem. Thank you! Michael